LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task # Using KIM Simulator Model : Sim_LAMMPS_SNAP_ChenDengTran_2017_Mo__SM_003882782678_000 # For Simulator : LAMMPS 12 Dec 2018 # Running on : LAMMPS 7 Aug 2019 # Lattice spacing in x,y,z = 3.15999 3.15999 3.15999 Created orthogonal box = (0 -41.3254 0) to (19.4795 41.3254 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.10094 5.07466 4.4689 Created 230 atoms create_atoms CPU = 0.00027585 secs 230 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.10094 5.07466 4.4689 Created 230 atoms create_atoms CPU = 0.000128031 secs 230 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXILIE5y/Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18 SNAP Element = Mo, Radius 0.5, Weight 1 Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXILIE5y/Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18 SNAP keyword rcutfac 4.615858 SNAP keyword twojmax 6 System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.61586 ghost atom cutoff = 6.61586 binsize = 3.30793, bins = 6 25 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 452 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.61586 ghost atom cutoff = 6.61586 binsize = 3.30793, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.756 | 4.756 | 4.756 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10079.035 0 -10079.035 7134.5748 35 0 -10106.281 0 -10106.281 1894.815 Loop time of 4.92846 on 1 procs for 35 steps with 452 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10079.0352982 -10106.2756128 -10106.2806274 Force two-norm initial, final = 49.1005 0.240718 Force max component initial, final = 15.8234 0.0695109 Final line search alpha, max atom move = 1 0.0695109 Iterations, force evaluations = 35 60 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9247 | 4.9247 | 4.9247 | 0.0 | 99.92 Neigh | 0.0012949 | 0.0012949 | 0.0012949 | 0.0 | 0.03 Comm | 0.0015271 | 0.0015271 | 0.0015271 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009224 | | | 0.02 Nlocal: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3040 ave 3040 max 3040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29064 ave 29064 max 29064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29064 Ave neighs/atom = 64.3009 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.761 | 4.761 | 4.761 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -10106.281 0 -10106.281 1894.815 7194.8947 37 0 -10106.293 0 -10106.293 563.25366 7198.6003 Loop time of 0.337095 on 1 procs for 2 steps with 452 atoms 100.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10106.2806274 -10106.2912086 -10106.2928971 Force two-norm initial, final = 19.6136 1.62953 Force max component initial, final = 19.4345 1.57138 Final line search alpha, max atom move = 0.000133628 0.000209981 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33679 | 0.33679 | 0.33679 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.0824e-05 | 8.0824e-05 | 8.0824e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002263 | | | 0.07 Nlocal: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3084 ave 3084 max 3084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29024 ave 29024 max 29024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29024 Ave neighs/atom = 64.2124 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.61586 ghost atom cutoff = 6.61586 binsize = 3.30793, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (3) compute pair/local, occasional, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.392 | 4.392 | 4.392 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10106.293 0 -10106.293 563.25366 Loop time of 1.19209e-06 on 1 procs for 0 steps with 452 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.192e-06 | | |100.00 Nlocal: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3084 ave 3084 max 3084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29024 ave 29024 max 29024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29024 Ave neighs/atom = 64.2124 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.392 | 4.392 | 4.392 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -10106.293 -10106.293 19.501012 82.650736 4.4662618 563.25366 563.25366 350.12466 1260.6916 78.94469 2.4913896 394.07534 Loop time of 9.53674e-07 on 1 procs for 0 steps with 452 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3084 ave 3084 max 3084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14512 ave 14512 max 14512 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29024 ave 29024 max 29024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29024 Ave neighs/atom = 64.2124 Neighbor list builds = 0 Dangerous builds = 0 452 -2297.6331772148 eV 2.49138957984704 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05